2 Input files

2.1 Negative control

## Taking input= as a system command ('gunzip -c ./input/NC_rep1.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
## compressing the file with bgzip...
## making tabix index...
## Taking input= as a system command ('gunzip -c ./input/NC_rep2.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
## compressing the file with bgzip...
## making tabix index...
## Taking input= as a system command ('gunzip -c ./input/NC_rep3.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
## compressing the file with bgzip...
## making tabix index...
## Taking input= as a system command ('gunzip -c ./input/NC_rep4.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
## compressing the file with bgzip...
## making tabix index...
## Taking input= as a system command ('gunzip -c ./input/NC_rep5.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
## compressing the file with bgzip...
## making tabix index...
## Taking input= as a system command ('gunzip -c ./input/NC_rep6.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
## compressing the file with bgzip...
## making tabix index...
## compressing the file with bgzip...
## making tabix index...
## flatfile located at: /mnt/IM/DKT/courses/sta426-project-dmr-comparison/exp/20181125-differential_analysis_regions-02/20181206-06_methylKit/output/methylDB/methylBase_734d13f4dd63.txt.bgz

2.2 Simulated data

## Taking input= as a system command ('gunzip -c ./input/sim_rep1.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
## compressing the file with bgzip...
## making tabix index...
## Taking input= as a system command ('gunzip -c ./input/sim_rep2.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
## compressing the file with bgzip...
## making tabix index...
## Taking input= as a system command ('gunzip -c ./input/sim_rep3.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
## compressing the file with bgzip...
## making tabix index...
## Taking input= as a system command ('gunzip -c ./input/sim_rep4.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
## compressing the file with bgzip...
## making tabix index...
## Taking input= as a system command ('gunzip -c ./input/sim_rep5.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
## compressing the file with bgzip...
## making tabix index...
## Taking input= as a system command ('gunzip -c ./input/sim_rep6.cov.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure envionment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
## compressing the file with bgzip...
## making tabix index...
## compressing the file with bgzip...
## making tabix index...
## flatfile located at: /mnt/IM/DKT/courses/sta426-project-dmr-comparison/exp/20181125-differential_analysis_regions-02/20181206-06_methylKit/output/methylDB/methylBase_734d4fba7119.txt.bgz

3 DMR analysis

3.1 Negative control

## checking wether tabix file already exists:
## ./output/methylDB/NC_rep1_tiled.txt.bgz
## tabix file is new.
## continuing now ...
## compressing the file with bgzip...
## making tabix index...
## checking wether tabix file already exists:
## ./output/methylDB/NC_rep2_tiled.txt.bgz
## tabix file is new.
## continuing now ...
## compressing the file with bgzip...
## making tabix index...
## checking wether tabix file already exists:
## ./output/methylDB/NC_rep3_tiled.txt.bgz
## tabix file is new.
## continuing now ...
## compressing the file with bgzip...
## making tabix index...
## checking wether tabix file already exists:
## ./output/methylDB/NC_rep4_tiled.txt.bgz
## tabix file is new.
## continuing now ...
## compressing the file with bgzip...
## making tabix index...
## checking wether tabix file already exists:
## ./output/methylDB/NC_rep5_tiled.txt.bgz
## tabix file is new.
## continuing now ...
## compressing the file with bgzip...
## making tabix index...
## checking wether tabix file already exists:
## ./output/methylDB/NC_rep6_tiled.txt.bgz
## tabix file is new.
## continuing now ...
## compressing the file with bgzip...
## making tabix index...
## compressing the file with bgzip...
## making tabix index...
## flatfile located at: /mnt/IM/DKT/courses/sta426-project-dmr-comparison/exp/20181125-differential_analysis_regions-02/20181206-06_methylKit/output/methylDB/methylBase_734d48bb96d8.txt.bgz
## two groups detected:
##  will calculate methylation difference as the difference of
## treatment (group: 1) - control (group: 0)
## checking wether tabix file already exists:
## /mnt/IM/DKT/courses/sta426-project-dmr-comparison/exp/20181125-differential_analysis_regions-02/20181206-06_methylKit/output/methylDB/methylDiff_734d48bb96d8.txt.bgz
## tabix file is new.
## continuing now ...
## compressing the file with bgzip...
## making tabix index...
## flatfile located at: /mnt/IM/DKT/courses/sta426-project-dmr-comparison/exp/20181125-differential_analysis_regions-02/20181206-06_methylKit/output/methylDB/methylDiff_734d48bb96d8.txt.bgz.bgz

3.2 Simulated data

## checking wether tabix file already exists:
## ./output/methylDB/sim_rep1_tiled.txt.bgz
## tabix file is new.
## continuing now ...
## compressing the file with bgzip...
## making tabix index...
## checking wether tabix file already exists:
## ./output/methylDB/sim_rep2_tiled.txt.bgz
## tabix file is new.
## continuing now ...
## compressing the file with bgzip...
## making tabix index...
## checking wether tabix file already exists:
## ./output/methylDB/sim_rep3_tiled.txt.bgz
## tabix file is new.
## continuing now ...
## compressing the file with bgzip...
## making tabix index...
## checking wether tabix file already exists:
## ./output/methylDB/sim_rep4_tiled.txt.bgz
## tabix file is new.
## continuing now ...
## compressing the file with bgzip...
## making tabix index...
## checking wether tabix file already exists:
## ./output/methylDB/sim_rep5_tiled.txt.bgz
## tabix file is new.
## continuing now ...
## compressing the file with bgzip...
## making tabix index...
## checking wether tabix file already exists:
## ./output/methylDB/sim_rep6_tiled.txt.bgz
## tabix file is new.
## continuing now ...
## compressing the file with bgzip...
## making tabix index...
## compressing the file with bgzip...
## making tabix index...
## flatfile located at: /mnt/IM/DKT/courses/sta426-project-dmr-comparison/exp/20181125-differential_analysis_regions-02/20181206-06_methylKit/output/methylDB/methylBase_734d50e7e64d.txt.bgz
## two groups detected:
##  will calculate methylation difference as the difference of
## treatment (group: 1) - control (group: 0)
## checking wether tabix file already exists:
## /mnt/IM/DKT/courses/sta426-project-dmr-comparison/exp/20181125-differential_analysis_regions-02/20181206-06_methylKit/output/methylDB/methylDiff_734d50e7e64d.txt.bgz
## tabix file is new.
## continuing now ...
## compressing the file with bgzip...
## making tabix index...
## flatfile located at: /mnt/IM/DKT/courses/sta426-project-dmr-comparison/exp/20181125-differential_analysis_regions-02/20181206-06_methylKit/output/methylDB/methylDiff_734d50e7e64d.txt.bgz.bgz

4 DMR Tables

4.1 Negative control

## Warning in instance$preRenderHook(instance): It seems your data is too
## big for client-side DataTables. You may consider server-side processing:
## https://rstudio.github.io/DT/server.html

4.2 Simulated data

## Warning in instance$preRenderHook(instance): It seems your data is too
## big for client-side DataTables. You may consider server-side processing:
## https://rstudio.github.io/DT/server.html

5 SessionInfo

## ─ Session info ──────────────────────────────────────────────────────────
##  setting  value                       
##  version  R version 3.5.1 (2018-07-02)
##  os       Ubuntu 16.04.5 LTS          
##  system   x86_64, linux-gnu           
##  ui       X11                         
##  language (EN)                        
##  collate  en_US.UTF-8                 
##  ctype    en_US.UTF-8                 
##  tz       Europe/Zurich               
##  date     2018-12-19                  
## 
## ─ Packages ──────────────────────────────────────────────────────────────
##  package              * version   date       lib source        
##  assertthat             0.2.0     2017-04-11 [1] CRAN (R 3.5.1)
##  backports              1.1.3     2018-12-14 [1] CRAN (R 3.5.1)
##  bbmle                  1.0.20    2017-10-30 [1] CRAN (R 3.5.1)
##  bindr                  0.1.1     2018-03-13 [1] CRAN (R 3.5.1)
##  bindrcpp               0.2.2     2018-03-29 [1] CRAN (R 3.5.1)
##  Biobase                2.40.0    2018-10-04 [1] Bioconductor  
##  BiocGenerics         * 0.26.0    2018-10-04 [1] Bioconductor  
##  BiocParallel           1.14.2    2018-07-08 [1] Bioconductor  
##  Biostrings             2.48.0    2018-10-29 [1] Bioconductor  
##  bitops                 1.0-6     2013-08-17 [1] CRAN (R 3.5.1)
##  callr                  3.1.0     2018-12-10 [1] CRAN (R 3.5.1)
##  cli                    1.0.1     2018-09-25 [1] CRAN (R 3.5.1)
##  coda                   0.19-2    2018-10-08 [1] CRAN (R 3.5.1)
##  colorspace             1.3-2     2016-12-14 [1] CRAN (R 3.5.1)
##  crayon                 1.3.4     2017-09-16 [1] CRAN (R 3.5.1)
##  crosstalk              1.0.0     2016-12-21 [1] CRAN (R 3.5.1)
##  data.table           * 1.11.8    2018-09-30 [1] CRAN (R 3.5.1)
##  DelayedArray           0.6.6     2018-09-11 [1] Bioconductor  
##  desc                   1.2.0     2018-05-01 [1] CRAN (R 3.5.1)
##  devtools               2.0.1     2018-10-26 [1] CRAN (R 3.5.1)
##  digest                 0.6.18    2018-10-10 [1] CRAN (R 3.5.1)
##  dplyr                  0.7.8     2018-11-10 [1] CRAN (R 3.5.1)
##  DT                   * 0.5       2018-11-05 [1] CRAN (R 3.5.1)
##  emdbook                1.3.10    2018-05-19 [1] CRAN (R 3.5.1)
##  evaluate               0.12      2018-10-09 [1] CRAN (R 3.5.1)
##  fastseg                1.26.0    2018-10-04 [1] Bioconductor  
##  fs                     1.2.6     2018-08-23 [1] CRAN (R 3.5.1)
##  GenomeInfoDb         * 1.16.0    2018-10-04 [1] Bioconductor  
##  GenomeInfoDbData       1.1.0     2018-10-04 [1] Bioconductor  
##  GenomicAlignments      1.16.0    2018-10-04 [1] Bioconductor  
##  GenomicRanges        * 1.32.7    2018-09-20 [1] Bioconductor  
##  ggplot2                3.1.0     2018-10-25 [1] CRAN (R 3.5.1)
##  glue                   1.3.0     2018-07-17 [1] CRAN (R 3.5.1)
##  gtable                 0.2.0     2016-02-26 [1] CRAN (R 3.5.1)
##  gtools                 3.8.1     2018-06-26 [1] CRAN (R 3.5.1)
##  htmltools              0.3.6     2017-04-28 [1] CRAN (R 3.5.1)
##  htmlwidgets            1.3       2018-09-30 [1] CRAN (R 3.5.1)
##  httpuv                 1.4.5     2018-07-19 [1] CRAN (R 3.5.1)
##  IRanges              * 2.14.12   2018-09-20 [1] Bioconductor  
##  jsonlite               1.6       2018-12-07 [1] CRAN (R 3.5.1)
##  knitr                  1.21      2018-12-10 [1] CRAN (R 3.5.1)
##  later                  0.7.5     2018-09-18 [1] CRAN (R 3.5.1)
##  lattice                0.20-38   2018-11-04 [1] CRAN (R 3.5.1)
##  lazyeval               0.2.1     2017-10-29 [1] CRAN (R 3.5.1)
##  limma                  3.36.5    2018-09-20 [1] Bioconductor  
##  magrittr               1.5       2014-11-22 [1] CRAN (R 3.5.1)
##  MASS                   7.3-51.1  2018-11-01 [1] CRAN (R 3.5.1)
##  Matrix                 1.2-15    2018-11-01 [1] CRAN (R 3.5.1)
##  matrixStats            0.54.0    2018-07-23 [1] CRAN (R 3.5.1)
##  mclust                 5.4.2     2018-11-17 [1] CRAN (R 3.5.1)
##  memoise                1.1.0     2017-04-21 [1] CRAN (R 3.5.1)
##  methylKit            * 1.6.3     2018-10-12 [1] Bioconductor  
##  mime                   0.6       2018-10-05 [1] CRAN (R 3.5.1)
##  munsell                0.5.0     2018-06-12 [1] CRAN (R 3.5.1)
##  numDeriv               2016.8-1  2016-08-27 [1] CRAN (R 3.5.1)
##  pillar                 1.3.1     2018-12-15 [1] CRAN (R 3.5.1)
##  pkgbuild               1.0.2     2018-10-16 [1] CRAN (R 3.5.1)
##  pkgconfig              2.0.2     2018-08-16 [1] CRAN (R 3.5.1)
##  pkgload                1.0.2     2018-10-29 [1] CRAN (R 3.5.1)
##  plyr                   1.8.4     2016-06-08 [1] CRAN (R 3.5.1)
##  prettyunits            1.0.2     2015-07-13 [1] CRAN (R 3.5.1)
##  processx               3.2.1     2018-12-05 [1] CRAN (R 3.5.1)
##  promises               1.0.1     2018-04-13 [1] CRAN (R 3.5.1)
##  ps                     1.2.1     2018-11-06 [1] CRAN (R 3.5.1)
##  purrr                  0.2.5     2018-05-29 [1] CRAN (R 3.5.1)
##  qvalue                 2.12.0    2018-11-28 [1] Bioconductor  
##  R.methodsS3            1.7.1     2016-02-16 [1] CRAN (R 3.5.1)
##  R.oo                   1.22.0    2018-04-22 [1] CRAN (R 3.5.1)
##  R.utils                2.7.0     2018-08-27 [1] CRAN (R 3.5.1)
##  R6                     2.3.0     2018-10-04 [1] CRAN (R 3.5.1)
##  Rcpp                   1.0.0     2018-11-07 [1] CRAN (R 3.5.1)
##  RCurl                  1.95-4.11 2018-07-15 [1] CRAN (R 3.5.1)
##  remotes                2.0.2     2018-10-30 [1] CRAN (R 3.5.1)
##  reshape2               1.4.3     2017-12-11 [1] CRAN (R 3.5.1)
##  rlang                  0.3.0.1   2018-10-25 [1] CRAN (R 3.5.1)
##  rmarkdown              1.11      2018-12-08 [1] CRAN (R 3.5.1)
##  rprojroot              1.3-2     2018-01-03 [1] CRAN (R 3.5.1)
##  Rsamtools              1.32.3    2018-08-22 [1] Bioconductor  
##  rtracklayer            1.40.6    2018-08-31 [1] Bioconductor  
##  S4Vectors            * 0.18.3    2018-10-04 [1] Bioconductor  
##  scales                 1.0.0     2018-08-09 [1] CRAN (R 3.5.1)
##  sessioninfo            1.1.1     2018-11-05 [1] CRAN (R 3.5.1)
##  shiny                  1.2.0     2018-11-02 [1] CRAN (R 3.5.1)
##  stringi                1.2.4     2018-07-20 [1] CRAN (R 3.5.1)
##  stringr                1.3.1     2018-05-10 [1] CRAN (R 3.5.1)
##  SummarizedExperiment   1.10.1    2018-10-04 [1] Bioconductor  
##  testthat               2.0.1     2018-10-13 [1] CRAN (R 3.5.1)
##  tibble                 1.4.2     2018-01-22 [1] CRAN (R 3.5.1)
##  tidyselect             0.2.5     2018-10-11 [1] CRAN (R 3.5.1)
##  usethis                1.4.0     2018-08-14 [1] CRAN (R 3.5.1)
##  withr                  2.1.2     2018-03-15 [1] CRAN (R 3.5.1)
##  xfun                   0.4       2018-10-23 [1] CRAN (R 3.5.1)
##  XML                    3.98-1.16 2018-08-19 [1] CRAN (R 3.5.1)
##  xtable                 1.8-3     2018-08-29 [1] CRAN (R 3.5.1)
##  XVector                0.20.0    2018-10-04 [1] Bioconductor  
##  yaml                   2.2.0     2018-07-25 [1] CRAN (R 3.5.1)
##  zlibbioc               1.26.0    2018-10-04 [1] Bioconductor  
## 
## [1] /home/ubuntu/R/x86_64-pc-linux-gnu-library/3.5
## [2] /usr/local/lib/R/site-library
## [3] /usr/lib/R/site-library
## [4] /usr/lib/R/library